A major goal of research in cyclic nucleotides is to study the biochemistry of enzymes, proteins and compounds which involve synthesis and degradation of the cyclic nucleotides and to link this knowledge to the understanding of the physiological functions in given tissues. The activity of cyclic AMP and cyclic GMP phosphodiesterase (PDE) and the protein activator of cyclic AMP phosphodiesterase in various anatomic and subcellular fractions of the bovine eye were studied. A heat-stable, non-dialyzable inhibitory factor of cyclic nucleotide phosphodiesterase was detected in and partially purified from bovine retina. The factor appears to be a protein. A small dialyzable molecular phosphodiesterase inhibitor was also isolated from bovine brain. This inhibitor is not a protein since it is not hydrolyzed by different proteolytic enzymes. The activities of cyclic nucleotide PDE and protein activator were measured in Brown-Pearce (rabbit) carcinoma before and after methotrexate perfusion. The differences in enzyme and activator activities were observed before and after the treatment of methotrexate. An abnormality in retinal cyclic nucleotide metabolism in inherited rod-cone dysplasia of Irish setter dog was observed.